Megabus typically only sells a couple seats at the bargain basement $1 fare. (There's also a $2.50/purchase fee for ticketing, at least when buying online.) Megabus' typical fares for that route seem to be $5-$20, with each Friday and Sunday often going quickly to $20 once one or two $1 tickets are sold. Last minute tickets and popular times/days can also get higher than $20.
On the Northeast Corridor, I'm not aware of anything Amtrak has outright cut, and they've recently improved cafe car offerings and refurbished the interiors of the trains. Megabus has a lot tighter and narrower seating, no food offerings at all, wifi that seems to work less well than even Amtrak's offering, and power outlets that usually work. I'd also much rather use an Amtrak bathroom than a Megabus bathroom.
There's certainly some instances where I'd take Megabus, but if money allows I'd certainly take Amtrak over Megabus in the NEC.
